Contacts of the helix formed by residues 599 - 620 (chain B) in PDB entry 2H3W
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 599 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408B ASP* 3.7 10.5 + - - -
574B TYR* 2.9 15.0 + - - +
598B THR* 1.3 77.7 + - - +
600B ALA* 1.3 67.0 + - - +
601B ALA* 3.2 13.7 + - - +
602B ARG* 2.9 41.9 + - + +
603B MET 2.9 18.7 + - - -
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Residues in contact with ALA 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408B ASP* 3.0 36.7 + - - +
410B MET* 3.6 12.1 - - + +
574B TYR* 3.9 4.4 - - - -
589B VAL* 3.5 38.7 - - + +
591B ALA* 4.0 4.1 - - + +
599B ASN* 1.3 70.7 - - - +
601B ALA* 1.3 58.4 + - - +
603B MET* 3.3 2.1 + - - +
604B ALA* 2.9 31.0 + - - +
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Residues in contact with ALA 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ASP* 4.7 1.8 + - - +
410B MET* 3.4 35.7 - - + +
599B ASN* 3.2 10.2 + - - +
600B ALA* 1.3 77.1 - - - +
602B ARG* 1.3 57.9 + - - +
604B ALA* 3.3 1.4 + - - +
605B HIS* 2.9 48.0 + - + -
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Residues in contact with ARG 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B ARG 5.7 0.2 + - - -
444B ILE* 3.1 39.2 + - + +
574B TYR* 5.6 0.9 - - - +
599B ASN* 2.9 31.3 + - + +
601B ALA* 1.3 69.8 - - - +
603B MET* 1.3 68.3 + - - +
605B HIS* 3.1 9.7 + - - +
606B TYR* 3.0 68.4 + - + -
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Residues in contact with MET 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B LEU* 4.2 19.1 - - - -
440B ALA* 4.7 4.3 - - - -
441B TYR* 3.6 29.8 - - + -
444B ILE* 4.1 17.9 - - + +
445B TYR* 4.1 8.1 - - + -
551B LEU* 4.4 3.8 - - + -
574B TYR* 3.2 66.2 + - + +
576B ILE* 4.3 9.4 - - + -
589B VAL* 4.1 10.5 - - + -
599B ASN 2.9 6.9 + - - +
600B ALA 3.7 3.4 - - - +
602B ARG* 1.3 76.1 - - - +
604B ALA* 1.3 62.5 + - - +
606B TYR* 3.4 1.4 + - - -
607B LEU* 3.0 25.0 + - + +
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Residues in contact with ALA 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B MET* 3.7 21.1 - - + -
412B LEU* 3.6 26.4 - - + +
589B VAL* 4.1 17.9 - - + +
600B ALA 2.9 18.1 + - - +
601B ALA 3.6 4.0 - - - +
603B MET* 1.3 76.9 - - - +
605B HIS* 1.3 61.9 + - + +
607B LEU* 3.2 7.6 + - - +
608B GLU* 3.0 24.8 + - - +
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Residues in contact with HIS 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B MET* 5.1 7.9 - - + +
412B LEU* 6.3 2.5 - - + -
601B ALA* 2.9 42.7 + - + +
602B ARG* 3.5 9.1 - - - +
604B ALA* 1.3 80.3 - - + +
606B TYR* 1.3 66.9 + - + +
608B GLU* 3.4 18.0 + - - +
609B LYS* 3.1 23.2 + - - +
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Residues in contact with TYR 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B ALA* 3.4 11.5 - - + +
443B ARG* 3.8 38.6 + - + -
444B ILE* 3.3 34.8 - - + -
602B ARG* 3.0 65.8 + - + +
603B MET 3.9 1.3 - - - +
605B HIS* 1.3 81.8 - - + +
607B LEU* 1.3 57.6 + - - +
609B LYS* 3.8 6.6 - - + +
610B ALA* 2.8 31.4 + - - +
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Residues in contact with LEU 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B LEU* 4.6 5.8 - - + -
433B ILE* 4.6 3.6 - - + +
436B ALA* 4.2 3.6 - - + -
437B LEU* 3.8 42.8 - - + +
440B ALA* 3.6 8.7 - - + +
576B ILE* 4.8 11.7 - - + -
587B PHE* 3.6 40.2 - - + -
589B VAL* 5.0 9.2 - - + -
603B MET* 3.0 18.2 + - + +
604B ALA 3.4 4.0 - - - +
605B HIS 3.1 0.2 - - - -
606B TYR* 1.3 79.0 - - - +
608B GLU* 1.3 63.2 + - - +
610B ALA* 3.1 2.9 + - - +
611B LEU* 2.9 44.1 + - + +
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Residues in contact with GLU 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B LEU* 4.2 22.3 - - + +
414B PHE* 3.5 30.7 - - + -
415B HIS* 4.9 3.1 - - - -
416B HIS* 2.7 29.6 + - + +
604B ALA 3.0 12.8 + - - +
605B HIS* 3.7 18.6 - - - +
607B LEU* 1.3 77.3 - - - +
609B LYS* 1.3 63.2 + - - +
611B LEU* 3.3 2.1 + - - -
612B LEU* 3.0 33.7 + - + +
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Residues in contact with LYS 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B ARG* 4.3 6.0 - - - +
605B HIS 3.1 16.8 + - - +
606B TYR* 3.9 7.4 - - + +
608B GLU* 1.3 75.7 - - - +
610B ALA* 1.3 61.1 + - - +
612B LEU* 3.3 13.5 + - + -
613B ASP* 2.8 63.9 + - - +
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Residues in contact with ALA 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B ALA* 3.3 28.9 - - - +
439B LEU* 3.9 14.9 - - + +
440B ALA* 3.9 8.5 - - + +
443B ARG* 3.9 12.5 - - - +
606B TYR 2.8 20.0 + - - +
607B LEU 3.4 4.5 - - - +
609B LYS* 1.3 77.9 - - - +
611B LEU* 1.3 61.4 + - - +
613B ASP* 3.2 2.3 + - - +
614B MET* 3.0 28.4 + - - +
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Residues in contact with LEU 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B PHE* 3.5 37.2 - - + -
417B PHE* 3.7 18.4 - - + -
432B PHE* 3.8 24.2 - - + -
433B ILE* 4.2 16.8 - - + +
436B ALA* 3.4 24.9 - - + -
585B ILE* 4.8 1.8 - - + -
587B PHE* 3.7 31.6 - - + -
607B LEU* 2.9 23.9 + - + +
608B GLU 3.5 2.9 - - - +
610B ALA* 1.3 77.7 - - - +
612B LEU* 1.3 60.4 + - - +
614B MET* 3.4 2.9 + - - +
615B ARG 3.2 16.8 + - - -
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Residues in contact with LEU 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B PHE* 3.8 7.9 - - + -
416B HIS* 3.4 53.6 - - + +
417B PHE* 4.2 3.6 - - + -
608B GLU* 3.0 28.5 + - + +
609B LYS* 3.7 14.8 - - + +
610B ALA 3.2 0.2 - - - -
611B LEU* 1.3 74.1 - - - +
613B ASP* 1.3 60.6 + - - +
615B ARG* 3.2 25.3 + - - +
616B THR* 2.9 33.4 + - - +
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Residues in contact with ASP 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B LEU* 5.0 0.2 - - + -
443B ARG* 2.7 42.4 + - - +
482B MET* 3.9 11.6 - - + +
609B LYS* 2.8 47.8 + - - +
610B ALA 3.7 3.6 - - - +
612B LEU* 1.3 76.6 - - - +
614B MET* 1.3 58.3 + - - +
616B THR* 3.7 8.4 + - - -
617B LEU* 2.9 30.5 + - - +
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Residues in contact with MET 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B PHE* 3.6 46.2 - - + +
435B VAL* 3.7 20.0 - - + -
436B ALA* 3.4 36.1 - - - -
439B LEU* 4.2 7.9 - - + -
478B PHE* 3.9 25.1 - - + -
482B MET* 4.7 1.8 - - + -
496B LEU* 3.9 25.5 - - + +
500B VAL* 4.9 0.2 - - + -
610B ALA 3.0 14.1 + - - +
611B LEU 3.8 1.3 - - - +
612B LEU 3.2 0.2 - - - -
613B ASP* 1.3 76.5 - - - +
615B ARG* 1.3 63.2 + - - +
617B LEU* 3.7 2.8 - - - +
618B LEU* 3.1 30.1 + - - +
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Residues in contact with ARG 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B HIS* 3.6 20.0 + - - +
417B PHE* 3.5 38.1 - - + +
421B PHE* 3.5 40.4 - - + -
432B PHE* 4.2 0.6 - - - -
611B LEU 3.2 12.2 + - - +
612B LEU* 3.2 29.2 + - - +
614B MET* 1.3 75.6 - - - +
616B THR* 1.3 62.2 + - - +
618B LEU* 3.2 2.3 + - - +
619B GLN* 2.8 52.5 + - - +
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Residues in contact with THR 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612B LEU* 2.9 18.9 + - - +
613B ASP* 3.4 9.7 + - - -
615B ARG* 1.3 77.0 + - - +
617B LEU* 1.3 63.3 + - - +
619B GLN* 3.3 9.9 + - - +
620B ASN* 2.9 51.0 + - - +
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Residues in contact with LEU 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478B PHE* 4.6 0.2 - - + -
482B MET* 4.0 21.3 - - + -
489B GLU* 3.9 31.2 - - + +
492B LYS* 3.8 29.4 - - + +
493B VAL* 3.7 14.3 - - + +
496B LEU* 3.9 22.4 - - + -
613B ASP 2.9 17.9 + - - +
614B MET 3.7 3.4 - - - +
616B THR* 1.3 76.9 - - - +
618B LEU* 1.3 63.0 + - - +
620B ASN* 3.2 7.6 + - - -
621B HIS* 3.2 43.0 + - + +
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Residues in contact with LEU 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421B PHE* 3.6 18.4 - - + -
425B GLU* 4.0 24.2 - - + +
427B LEU* 3.8 17.0 - - + -
432B PHE* 3.6 28.0 - - + -
493B VAL* 4.0 27.1 - - + -
496B LEU* 3.9 25.1 - - + -
497B ARG* 4.4 10.4 + - - +
614B MET 3.1 19.3 + - - +
615B ARG 3.7 3.1 - - - +
617B LEU* 1.3 79.4 - - - +
619B GLN* 1.3 63.3 + - - +
621B HIS 3.2 21.2 + - - +
622B PRO* 3.8 3.3 - - - +
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Residues in contact with GLN 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421B PHE* 3.7 19.7 - - + -
425B GLU* 5.0 3.4 - - - +
615B ARG* 2.8 53.9 + - - +
616B THR* 3.8 8.1 + - - +
618B LEU* 1.3 73.0 - - - +
620B ASN* 1.3 65.0 + - - +
621B HIS 3.1 1.2 + - - -
622B PRO* 3.4 18.4 - - - +
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Residues in contact with ASN 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B GLU* 4.6 8.4 - - - +
616B THR* 2.9 41.4 + - - +
617B LEU* 3.7 6.3 - - - +
618B LEU 3.2 0.6 - - - -
619B GLN* 1.3 83.9 + - - +
621B HIS* 1.3 81.3 + - + +
622B PRO* 3.5 4.9 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il